In human conditions, chronic pain is associated with widespread anatomical changes in the brain. Nevertheless, little is known about the time course of these changes or the relationship of anatomical changes to perception and behaviour. In the present study, we use a rat model of neuropathic pain (spared nerve injury, SNI) and 7 T MRI to determine the longitudinal supraspinal changes associated with pain-like and anxiety-like behaviours. SNI rats and sham controls were scanned at seven time points, 1 week before surgery, 2 weeks after, and then once a month for 5 months. At each time point we performed behavioural tests, including thermal and mechanical sensitivity, and tests of locomotion and exploratory behaviour (open field and elevated plus maze). We found that SNI rats had early and sustained thermal and mechanical hyperalgesia, and developed anxiety-like behaviours several months after injury. Compared to sham controls, SNI rats had decreased frontal cortex volumes several months after surgery, coincident with the onset of anxiety-like behaviours. There was also decreased volume in retrosplenial and entorhinal cortices. We also explored areas that correlated with mechanical hyperalgesia and found that increased hyperalgesia was associated with decreased volumes in bilateral S1 hindlimb area, anterior cingulate cortex (ACC, areas 32 and 24), and insula. Overall, our results suggest that long-term neuropathic pain has widespread effects on brain anatomy related to the duration and magnitude of the pain.